TABLE 2.
Putative ORFs in the SXT sequence
| ORF no. (gene name) | Coding region | Probable function | Identity (%/range)a | Homologyb
|
GI accession no. | Required for SXT transferc | |
|---|---|---|---|---|---|---|---|
| Gene name | Source | ||||||
| 001 (int) | 836-2074 | Integrase | 97/413 | int | R391 (P. rettgeri) | 12746566 | Y |
| 002 | 2079-2345 | Unknown | 93/79 | orf2 | R391 (P. rettgeri) | 12746565 | N |
| 003 | 2351-3322 | Unknown | 99/324 | orf1 | R391 (P. rettgeri) | 12746564 | N |
| 004 (rumB′) | 4244-5413 | UV repair DNA polymerase | 92/372 | rumB | R391 (P. rettgeri) (truncated) | 862633 | N |
| 005 (tnp) | 5697-6287 | Transposase | 41/178 | tnp | pPHGI (Pseudomonas putida) (truncated) | 4754812 | N |
| 006 (tnpA) | 6404-9301 | Transposase | 29/961 | tnpA | pPHGI (P. putida) | 7465523 | N |
| 007 (tnpB) | 9799-11289 | Transposase | 99/496 | orfA | E. coli | 10312101 | N |
| 008 (dfR18) | 11656-12207 | Dihydrofolate reductase type VIII | 59/157 | dhfRVIII | pLM0226 (E. coli) | 507215 | N |
| 009 | 12224-12766 | Unknown | 45/217 | mlr6191 | Mesorhizobium loti (truncated) | 14025924 | N |
| 010 | 12769-13932 | Unknown | N | ||||
| 011 (dcd) | 13950-14675 | Deoxycytidine triphosphate deaminase | 44/208 | dcd | Pseudomonas aeruginosa | 9949625 | N |
| 012 (′tnpB) | 14935-15264 | Transposase | 100/110 | orfA | E. coli (truncated) | 10312102 | N |
| 013 | 15298-16179 | Unknown | N | ||||
| 014 (floR) | 16399-17610 | Florfenicol exporter | 99/404 | floR | E. coli | 10312100 | N |
| 015 | 17641-17943 | Transcriptional repressor | 70/100 | orf1 | S. enterica serovar Typhimurium DT104 (truncated) | 12719030 | N |
| 016 (tnpB′) | 18058-18594 | Transposase | 100/135 | orfA | E. coli (truncated) | 10312101 | N |
| 017 (strB) | 18572-19405 | Streptomycin phosphotransferase | 100/278 | strB | Tn5393 (Erwinia amylovora) | 420965 | N |
| 018 (strA) | 19408-20022 | Streptomycin phosphotransferase | 99/267 | strA | Tn5393 (E. amylovora) | 420964 | N |
| 019 (sulII) | 20272-21084 | Dihydropteroate synthase type II | 100/271 | sulII | RSF1010 (E. coli) | 118596 | N |
| 020 (tnpA′) | 21555-22914 | Transposase | 24/413 | tnpA | pPHG1 (P. putida) (truncated) | 7465523 | N |
| 021 | 22639-23358 | Methyl-directed mismatch DNA repair | 51/173 | mutL | V. cholerae (truncated) | 127554 | N |
| 022 (′rumB) | 23514-23831 | DNA polymerase UV repair | 98/78 | rumB | R391 (P. rettgeri) (truncated) | 862633 | N |
| 023 (rumA) | 23791-24162 | UV repair | 98/149 | rumA | R391 (P. rettgeri) | 862632 | N |
| 024 | 24876-25781 | Polymerase epsilon subunit | 90/250 | R391 (P. rettgeri) | 13992587 | N | |
| 025 | 25858-26169 | Unknown | N | ||||
| 026 | 26241-27164 | Unknown | 36/261 | nmaI157 | Neisseria meningitides (group A strain Z2491) | 11281285 | N |
| 027 | 27395-27775 | Unknown | N | ||||
| 028 | 27766-28356 | Unknown | N | ||||
| 029 | 28378-30270 | Unknown | N | ||||
| 030 | 30325-31920 | Unknown | N | ||||
| 031 | 32037-32570 | DNA recombination | 35/64 | orf1 | pNSF-1 (Shigella flexneri) | 12034665 | N |
| 032 | 32488-33237 | Unknown | 25/182 | ss01994 | Sulfolobus solfataricus (truncated) | 13815272 | N |
| 033 | 33237-33992 | Unknown | N | ||||
| 034 | 34209-34676 | Unknown | N | ||||
| 035 | 34672-35868 | Unknown | N | ||||
| 036 | 35852-36229 | Unknown | N | ||||
| 037 | 36399-37010 | Unknown | N | ||||
| 038 | 37601-40231 | Unknown | N | ||||
| 039 | 40251-42323 | Lon protease | 28/165 | lon | Thermus thermophilus (truncated) | 9719397 | N |
| 040 | 42331-45018 | Unknown | 25/912 | orf74 | pB171 (E. coli) | 10955424 | N |
| 041 (traI) | 45176-47323 | Relaxase | 26/314 | xf1753 | Xylella fastidiosa | 11361836 | Y |
| 042 (traD) | 47396-49192 | Coupling factor | 29/536 | traG | R27 (S. enterica serovar Typhi) | 10957308 | Y |
| 043 | 49753-50385 | Coupling factor | 29/96 | r0117 | R27 (S. enterica serovar Typhi) | 10957306 | Y |
| 044 | 50417-50692 | Unknown | 37/82 | gp48 | Bacteriophage N15 | 9630515 | N |
| 045 | 50692-51012 | Unknown | 40/102 | gp49 | Bacteriophage N15 | 9630516 | N |
| 046 (traL) | 51187-51471 | Sex pilus assembly | 23/72 | traL | pNL1 (S. aromaticivorans) | 10956948 | Y* |
| 047 (traE) | 51471-52094 | Sex pilus assembly | 26/171 | trhE | R27 (S. enterica serovar Typhi) | 10957221 | Y* |
| 048 | 52078-52974 | Unknown | 25/254 | r0031 | R27 (S. enterica serovar Typhi) | 10957220 | Y* |
| 049 (traB) | 52980-54266 | Sex pilus assembly | 40/209 | trhB | R27 (S. enterica serovar Typhi) | 10957218 | Y* |
| 050 (traV) | 54266-54913 | Sex pilus assembly | 23/126 | trhV | R27 (S. enterica serovar Typhi) | 10957215 | Y* |
| 051 (traA) | 54913-55296 | Pilin subunit | 24/85 | trhA | R27 (S. enterica serovar Typhi) | 10957223 | Y |
| 052 (ynd) | 55664-56308 | Unknown | 46/296 | ynd | pTi (A. tumefaciens) | 10955130 | N |
| 053 (ync) | 56292-57239 | Unknown | 36/108 | ync | pTi (A. tumefaciens) | 10955129 | N |
| 054 (dsbC) | 57374-58063 | Thiol-disulfide interchange | 27/192 | dsbC | P. aeruginosa PAO1 | 9949905 | Y* |
| 055 (traC) | 58066-60462 | Sex pilus assembly | 27/869 | trhC | R27 (S. enterica serovar Typhi) | 10957214 | Y* |
| 056 (trsF) | 60789-61298 | Conjugation signal peptidase | 28/127 | trhF | R27 (S. enterica serovar Typhi) | 10957198 | Y* |
| 057 (traW) | 61312-62433 | Sex pilus assembly | 28/303 | trhW | R27 (S. enterica serovar Typhi) | 10957197 | Y* |
| 058 (traU) | 62420-63445 | Sex pilus assembly | 36/316 | trhU | R27 (S. enterica serovar Typhi) | 10957196 | Y* |
| 059 (traN) | 63683-67144 | Mating pair stabilization | 25/481 | trhN | R27 (S. enterica serovar Typhi) | 10957195 | Y* |
| 060 | 67927-69006 | Unknown | N | ||||
| 061 | 69009-70070 | Unknown | N | ||||
| 062 | 70186-70899 | Nuclease | 53/205 | nucM | Pectobacterium chrysanthemi | 403002 | N |
| 063 | 71011-71610 | Unknown | N | ||||
| 064 (ssb) | 72318-72734 | SSB | 38/135 | ssb | Plasmid F (E. coli) | 8918883 | N |
| 065 (bet) | 72817-73632 | DNA recombination | 55/195 | bet | Bacteriophage 933W | 9632480 | N |
| 066 (gp47) | 73921-74934 | Unknown | 25/255 | gp47 | Bacteriophage A118 | 5823649 | N |
| 067 (cobS) | 75030-76103 | Porphyrin biosynthesis | 31/288 | cobS | pMT1 (Yersinia pestis) | 3883103 | N |
| 068 | 76975-77925 | Unknown | 20/205 | r0207 | R27 (S. enterica serovar Typhi) | 10957394 | N |
| 069 | 77990-78427 | Unknown | N | ||||
| 070 | 78500-80152 | Unknown | 20/265 | r0206 | R27 (S. enterica serovar Typhi) | 10957393 | N |
| 071 (radC) | 80237-80731 | DNA repair | 56/151 | radC | V. cholerae | 11355878 | N |
| 072 | 81243-82241 | Unknown | 36/232 | r0204 | R27 (S. enterica serovar Typhi) | 10957391 | N |
| 073 | 82335-83039 | Unknown | N | ||||
| 074 | 83307-84233 | Response regulator | 39/289 | rrp-1 | Borrelia burgdorferi | 2688314 | N |
| 075 | 84242-88045 | Histidine kinase | 37/1233 | pa4112 | P. aeruginosa PAO1 | 11351830 | N |
| 076 (traF) | 88747-89721 | Sex pilus assembly | 27/278 | r0126 | R27 (S. enterica serovar Typhi) | 10957315 | ND |
| 077 (traH) | 89727-91112 | Sex pilus assembly | 39/451 | trhH | R27 (S. enterica serovar Typhi) | 10957316 | ND |
| 078 (traG) | 91119-94685 | Sex pilus assembly | 21/828 | traG | R27 (S. enterica serovar Typhi) | 10956931 | Y |
| 079 | 94724-95173 | Unknown | N | ||||
| 080 (setC) | 95210-95740 | Transcriptional activator | 31/172 | s006 | DT104 (S. enterica serovar Typhimurium) | 12719014 | Y |
| 081 (setD) | 95740-96036 | Flagellar transcriptional activator | 28/97 | flhD | Serratia liquefaciens | 2126176 | Y |
| 082 | 96036-96581 | Unknown | 29/130 | mlr2934 | M. loti | 13472590 | N |
| 083 | 96571-96936 | Unknown | N | ||||
| 084 | 96929-97231 | Unknown | N | ||||
| 085 | 97221-97739 | Unknown | N | ||||
| 085 (ydaS) | 98147-98395 | Unknown | 42/59 | ydaS | Prophage CP-933N (E. coli) | 12514682 | UNK |
| 086 (setR) | 98513-99157 | Transcriptional repressor | 46/213 | cl | Phage 434 | 420538 | UNK |
a
Identity is presented as percent amino acid identity between the SXT ORF and the best hit. The range is the number of amino acids over which this identity exists.
b
The number of identical amino acids of the respective gene products was determined by BLAST (1). The best hit and its source are presented.
c
Strains containing single deletions or deletions of multiple genes were scored for the ability to transfer SXT in a mating assay (Table 3). A strain was scored N if transconjugants were observed, Y if transconjugants were not observed, Y* if the gene was part of a larger deletion in which transconjugants were not observed, ND if the deletion was not constructed, and UNK if a single deletion could not be obtained.